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NovaSeq 6000 System


NovaSeq 6000 System

The NovaSeq 6000 System unleashes a new era in sequencing with groundbreaking innovations, providing users with the throughput, speed, and flexibility to complete projects faster and more economically than ever before. Leveraging proven Illumina next-generation sequencing (NGS) technology, multiple flow cell types, two library loading workflows, and various read length combinations, the NovaSeq 6000 System enables effective throughput scaling to suit virtually any study needs. Applications requiring large amounts of data, such as human whole- genome sequencing (WGS), ultradeep exome sequencing, and tumor–normal profiling can now be completed in a more cost effective manner.

Flexible Performance:

The NovaSeq 6000 System offers tremendous flexibility in sequencing options, supporting an extensive output range. Users can mix and match between four flow cell types (SP, S1, S2, or S4), run one or two flow cells at a time, and choose between multiple read lengths to easily adjust output and sample throughput for each sequencing run.

Common sequencing methods Whole-genome sequencing Illumina DNA PCR-Free Prep Illumina DNA Prep

Targeted resequencing

Illumina DNA Prep with Enrichment + Illumina Exome Panel Illumina RNA Prep with Enrichment + Illumina Exome Panel RNA sequencing

Illumina Stranded Total RNA Prep with Ribo-Zero Plus Illumina Stranded mRNA Library Prep

Epigenetic sequencing TruSeq Methyl Capture EPIC Unique dual indexing

IDT for Illumina DNA/RNA UD Indexes, Tagmentation (384 indexes across Sets A-D)


Popular Applications & Methods:

Large Whole-Genome Sequencing (human, plant, animal)

Small Whole-Genome Sequencing (microbe, virus)

Exome & Large Panel Sequencing (enrichment-based)

Targeted Gene Sequencing (amplicon-based, gene panel)

Single-Cell Profiling (scRNA-Seq, scDNA-Seq, oligo tagging assays)

Transcriptome Sequencing (total RNA-Seq, mRNA-Seq, gene expression profiling)

Chromatin Analysis (ATAC-Seq, ChIP-Seq)

Methylation Sequencing

Metagenomic Profiling (shotgun metagenomics, metatranscriptomics)

Cell-Free Sequencing & Liquid Biopsy Analysis


Run Time ~13 – 38 hours (dual SP flow cells)
~13–25 hours (dual S1 flow cells)
~16–36 hours (dual S2 flow cells)
~44 hours (dual S4 flow cells)
Maximum Output 6000 Gb
Maximum Reads Per Run 20 billion
Maximum Read Length 2 x 250**

Instrument Specifications

Instrument configuration
  • Computer and touch screen display
  • Installation setup and accessories
  • Data collection and analysis software
Instrument control computer
  • Base Unit: Portwell WADE-8022 with Intel i7 4700EQ CPU
  • Memory: 2 × 8 GB DDR3L SODIMM
  • Hard Drive: None
  • Solid-State Drive: 256 GB mSATA
  • Operating System: Windows 10
  • Note: Computer configurations will be upgraded regularly; contact your local account manager for current configuration
Operating environment
  • Temperature: 19°C-25°C (22°C ±3°C), <2°C change per hour
  • Humidity: 20%-80% relative humidity, non-condensing
  • Altitude: Below 2000 meters (6500 feet)
  • Ventilation: Maximum of 8530 BTU/h and average 6000 BTU/h
  • For Indoor Use Only
  • Wavelengths: 532 nm, 660 nm, 780 nm, 790 nm
  • W × D × H: 80.0 cm (31.5 in) × 94.5 cm (37.2 in) × 165.6 cm (65.2 in) with monitor
  • Weight: 481 kg (1059 lb), includes 3.5 kg (7.8 lb) for leak tray and 0.9 kg (2 lb) for keyboard and mouse, Crated Weight: 628 kg (1385 lb)
Crated Dimensions
  • Crated W×D×H: 92 cm × 120 cm × 118 cm
  • Crated Weight: 232 kg
Power requirements
  • 200–240 VAC 50/60Hz, 16A, single phase, 2500 W
  • Illumina provides a region-specific uninterruptible power supply
Network connection
  • Dedicated 1 Gb connection between the instrument and data management system. Connect directly or through network
Bandwidth for network connection
  • 200 Mb/s/instrument for internal network uploads
  • 200 Mb/s/instrument for BaseSpace Sequence Hub uploads
  • 5 Mb/s/instrument for Instrument Operational Data uploads

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